Repository Index

Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

• jax

Eclipse SUMO is an open source, highly portable, microscopic and continuous traffic simulation package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a large set of tools for scenario creation.

• traffic
• simulation
• transport

POT : Python Optimal Transport

• optimal-transport
• numerical-optimization
• machine-learning
• emd

PyWavelets - Wavelet Transforms in Python

• wavelets
• wavelet-transform
• signal-processing
• image-processing

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis

The open source air traffic simulator

• python
• traffic
• aircraft
• simulation

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

A Python native dynamical system simulation framework in the block diagram paradigm.

• blockdiagram
• control-systems
• hierarchical-modeling
• nonlinear-dynamics

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

The repository host gives no description.

Schema and generated objects for biolink data model and upper ontology

• biolink
• monarchinitiative
• gene-ontology
• datamodel

The Complete Street Rule for ArcGIS CityEngine is a scenario oriented design tool intended to enable users to quickly create procedurally generated multimodal streets.

• complete
• streets
• transportation
• cityengine

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

Autonomous multi-agent framework to optimize scientific software

• acceleration
• agentic-ai
• ai-agents
• bioinformatics

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution

Generative models for transcriptomic-driven or protein-driven molecular design (PaccMann^RL).

• deep-reinforcement-learning
• generative-model
• vae
• molecule-generation